Bioanalytical instrumentation using a light source subsystem

ABSTRACT

The invention relates to a light source for irradiating molecules present in a detection volume with one or more selected wavelengths of light and directing the fluorescence, absorbance, transmittance, scattering onto one or more detectors. Molecular interactions with the light allow for the identification and quantitation of participating chemical moieties in reactions utilizing physical or chemical tags, most typically fluorescent and chromophore labels. The invention can also use the light source to separately and simultaneously irradiate a plurality of capillaries or other flow confining structures with one or more selected wavelengths of light and separately and simultaneously detect fluorescence produced within the capillaries or other flow confining structures. In various embodiments, the flow confining structures can allow separation or transportation of molecules and include capillary, micro bore and milli bore flow systems. The capillaries are used to separate molecules that are chemically tagged with appropriate fluorescent or chromophore groups.

PRIORITY CLAIM

This application claims priority to: (1) U.S. Provisional PatentApplication Ser. No: 60/802,883, entitled: “CAPILLARY ELECTROPHORESISLIGHT PIPE”, inventors: Claudia B. Jaffe et al., filed May 22, 2006; (2)U.S. Provisional Patent Application Ser. No: 60/831,011, entitled: “WELLLIGHT PIPE”, inventors: Claudia B. Jaffe et al., filed Jul. 14, 2006 and(3) U.S. States Provisional Patent Application Ser. No: 60/888,902,entitled: “CAPILLARY ELECTROPHORESIS LIGHT SOURCE SUBSYSTEM”, inventors:Claudia B. Jaffe et al., filed Feb. 8, 2007. These applications areherein expressly incorporated by reference in their entireties.

FIELD OF THE INVENTION

The present invention relates to luminescence systems for irradiatingbioanalytical instrumentation including wells containing chemicals forinducing reactions or detecting reactants or products of chemicalreactions. The bioanalytical instrumentation can include a light sourceand fiber optic systems for irradiating analytes within capillaries withselected wavelengths of light and detecting luminescence produced by theanalytes within the capillaries.

BACKGROUND OF THE INVENTION

The micro titer plate reader has been a workhorse for bioanalyticaltesting for decades. It enables the facile and rapid interrogation of anarray of chemical reactions. Typically 8 by 12 well formats of 96 wellsare filled with reagents and or products of a calorimetric orfluorescent reaction. Higher order formats include multiples of 96wells. Such micro-titer plates are exposed to light of a desiredwavelength and the interaction of the reacting species with the light isrecorded.

Reactions may be immunochemical, enzyme based, polymerizations,intercollations or any of the varied molecular biological andbiochemical systems investigated in the biochemists' laboratory. Theinteractions may include and are not limited to absorbance,transmittance, scatter and fluorescence. Micro titer plate readers aredesigned to generate one or more wavelengths of interest. Typically thelight is generated using a wide spectrum source, arc lamps and halogenbulbs with numerous filters or gratings are common design components.

Biochemical reactions formatted in either homogeneous or heterogeneousbased detection platforms are also performed in miniaturized systems,e.g. on micro fluidic chips and micro arrays. In miniaturized systems,reaction volumes are contained within channels and/or with carefullymodified surface chemistry to allow for a plethora of chemical andbiological analysis in small reaction volumes. The chemistry istypically interrogated using confocal microscopy or imaging to assessthe extent of higher density features. Tens to hundreds of thousands ofenzyme, immunochemical, nucleic acid and protein reactions can befollowed simultaneously. Lamp and lasers power the various detectionsystems designed to report on the extent of reaction.

One now commonplace procedure performed in the bioanalytical laboratoryis the polymerase chain reaction (PCR). The technique has becomefundamental to molecular biology. It is one of a family of methods (i.e.reverse transcriptase PCR) for synthesizing a given quantity ofpre-selected biopolymer. PCR functions on DNA. In a typical experiment,the DNA of interest is separated into two complementary strands. Theends of each strand bind to a primer at the end where the synthesisbegins. The addition of the DNA polymerase initiates the synthesis of acomplementary strand on each single strand creating a doubling of theamount of DNA. The process is repeated until a sufficient number of DNAsegments have been synthesized. A unique temperature profile is used toadvance the reaction through the phases of separation (melting), primerbinding (annealing), and replication (extension). While the PCRtechnique has become a workhorse of the biotechnologist due to theenhanced sensitivity it offers over blotting techniques, PCR is notideally suited to quantitation. Small differences between sample sizescan become huge differences in final amplified material after multipledoublings.

A typical PCR reaction can be seen in three phases: an early lag phase,an exponential growth phase and a plateau region. The lag phase is aconsequence of the sensitivity of the instrument and the backgroundsignal of the probe system used to detect the PCR product. Theexponential growth phase commences when sufficient product hasaccumulated to be detected by the specific instrument. During thisexponential growth the amplification is described by Tn=Ti(E)n, where Tnis the amount of target sequence at cycle n, Ti is the initial amount oftarget material, and E is the efficiency of amplification. In the finalplateau phase the amplification efficiency drops as product competesmore effectively with primers for annealing and the amount of enzymebecomes limiting. The exponential equation no longer holds in theplateau phase. Most of the quantitative information is found in theexponential cycles but the exponential cycles typically comprise only 4or 5 cycles out of 40. For traditional PCR methods, identifying theexponential cycles requires the reaction be split into multiple reactiontubes that are assayed for PCR product after varying numbers of cycles.This requires either assaying many tubes or having a fairly good idea ofthe answer before the experiment is begun. Once the position of thisphase is determined the experimental phase can be compared to knownstandards and the copy number can be calculated.

Instrumentation advancements have made real-time monitoring of PCRreactions possible. Thermocycling is carried out using standardtechniques known to those skilled in the art, including rapid cyclingPCR. Fluorescence monitoring at each cycle for quantitative PCR wasdeveloped by Higuchi et al., “Simultaneous Amplification and Detectionof Specific DNA Sequences,” Bio. Technology, 10:413-417, 1992, which isherein expressly incorporated by reference in its entirety. Ethidiumbromide was used as the fluorescent entity. Fluorescence was acquiredonce per cycle for a relative measure of product concentration. Thecycle where observable fluorescence first appeared above the backgroundfluorescence correlated with the starting copy number, allowing theconstruction of a standard curve. Alternatively PCR amplification may beconducted with fluorescently labeled hybridization probes. Thehybridization probe system comprises two oligonucleotide probes thathybridize to adjacent regions of a DNA sequence wherein eacholigonucleotide probe is labeled with a respective member of afluorescent energy transfer pair. In this embodiment, the presence ofthe target nucleic acid sequence in a biological sample is detected bymeasuring fluorescent energy transfer between the two-labeledoligonucleotides. A number of strategies now exist using molecularbeacons or intercollating dyes all of which are strategies to increasesignal as a function of increasing DNA concentration as the synthesiscycles increase.

Such instrumentation and fluorescent monitoring techniques have madekinetic PCR significantly easier than traditional competitive PCR. Theease, accuracy and precision of quantitative PCR have all improved byallowing observation of the PCR product concentration at every cycle. Inthe Roche® Diagnostics embodiment of the kinetic PCR instrument, PCRreactions are conducted using the Light Cycler®, a real-time PCRinstrument that combines a rapid thermal cycler with a fluorimeter.Through the use of such a device, PCR product is detected withfluorescence and no additional sample processing, membrane arrays, gels,capillaries, or other analytical tools are necessary. Other PCRinstrumentation as known in the art may be used in the practice of thepresent invention.

Separation by electrophoresis is based on differences in solute velocityin an electric field. The velocity of a charged analyte is a function ofits electrophoretic mobility and the applied voltage. The method ofelectrophoresis is used in a number of different techniques includingcapillary gel electrophoresis, capillary zone electrophoresis, micellarelectrokinetic chromatography, capillary electro chromatography,isotachophoresis and isoelectric focusing.

In general, the mobility of an analyte in a particular medium isconstant and characteristic of that analyte. The analytes mobility is aresult of two factors. The analyte is attracted to the electrode ofopposite charge, pulling it through the medium. At the same time,however, frictional forces try to prevent the analyte moving toward thecharge. The balance of these forces determines the actual overallmobility of the analyte. An analytes size, polarity and number ofelectric charge(s), relative hydrophobicity and ionic strength determinehow rapidly an electric field can move the analyte through a medium. Abuffer is used to assist the flow of the analyte relative to the field.The buffer's chemical composition, pH, temperature and concentrationalter the mobility of the analyte. Many important biological moleculessuch as amino acids, peptides, proteins, nucleotides, and nucleic acids,posses ionizable groups and, therefore, at any given pH, exist insolution as electrically charged species either as cations containing apositive (+) charge or as anions containing a negative (−) charge.Depending on the nature of the net charge, the charged particles willmigrate either to the cathode or to the anode. A small analyte will haveless frictional drag than a large analyte and hence move through themedium faster than a large analyte. Similarly, a multiply chargedanalyte will experience more attraction to the electrode and also movethrough the medium faster than a singly charged analyte. It is thisdifference in solute velocities that is responsible for the separatingeffect in electrophoresis that results in resolution of the speciesdetected.

Gel electrophoresis is a method that separates molecules such as DNA orproteins on the basis of their physical properties. A gel is a solidcolloid. Thus, gel electrophoresis refers to the technique in whichmolecules are forced to cross a span of gel, motivated by an electricalcurrent. Activated electrodes at either end of the gel provide theelectric field and thus the driving force for the migration of theanalyte. During electrophoresis, molecules are forced to move throughthe pores in the gel when the electrical current is applied. Their rateof migration, through the induced electric field, depends on thestrength of the field, their charge, their size and the shape of themolecules, the relative hydrophobicity of the molecules, and on theionic strength and temperature of the buffer in which the molecules aremoving.

One use of gel electrophoresis is the identification of particular DNAmolecules by the band patterns they yield in gel electrophoresis, afterbeing cut with various restriction enzymes. Viral DNA, plasmid DNA, andparticular segments of chromosomal DNA can all be identified in thisway. Another use is the isolation and purification of individual DNAfragments containing interesting genes, which can be recovered from thegel with full biological activity.

Capillary Zone Electrophoresis (CZE) replaces the gel in gelelectrophoresis with the combination of a buffer and a solid supportcontained within the capillary. In CZE, the analyte must move throughthe solid support contained within the capillary under the action of thebuffer, which is charged by the applied electric field. The buffer'schemical nature, pH, temperature, concentration and the presence ofsurfactant additives can be selected to assist in fully resolving (i.e.,spatially separating different analytes in the capillary with respect tothe time from introduction of the sample) different analytes in space(position in the capillary) with respect to time. Analytes separated byCZE can be detected based on absorption or fluorescence. Detection canbe carried out using on-column or fiber optic Z-cells.

In addition to electrophoretic techniques, separation of molecules canbe carried out in the absence of an applied field using chromatographictechniques. In liquid chromatography, the molecule dissolved in a buffercan still be charged, but rather than an electric field creating thedriving force, molecule migration is dependent on the flow of thebuffer. Frictional forces due to the interaction of the molecule with asolid support present in a column, act to prevent the molecule frommoving with the buffer. The molecule's size, hydrophobicity, and ionicstrength determine how rapidly the buffer can move the molecule througha medium. The buffer's chemical composition, pH, temperature andconcentration together with the nature of the solid support dispersed inthe column alter the mobility of the molecule. High performance liquidchromatography (HPLC) utilizes pumps to increase the flow of bufferthrough the columns resulting in high column backpressure, improvedresolution, increased flow rates and reduced analysis times. By reducingthe diameter of the column and/or increasing the length of the columnthe resolution can be improved. However, a problem with narrower columns(milli bore or micro bore) involves detection of the eluted species. Asthe diameter of the capillary in the narrow bore HPLC systems is furtherreduced, only a small number of molecules are available for detection ina small-defined area.

Microfluidic systems comprised of microfluidic chips, automated reagentdelivery apparatus and detection instrumentation are designed tominimize the users' effort in reagent delivery, reagent dilution and/ormixing, initiating chemical reactions and detecting those chemicalreactions in small volumes within highly automated environments. Amongthe numerous applications that exist, fluorescence is a commonly useddetection format. It is a sensitive and robust method for detectingenzyme assays, immunoassays, polymerase chain reaction (PCR),quantitative PCR, genomic sequencing among many other important chemicalreactions. Both homogeneous and heterogeneous reactions are suited tosuch devices and analysis is not limited by whether the reaction takesplace in free solution or on a solid support or within a narrow pore.Often microfluidic devices are produced by etching, molding or embossingchannels and wells into solid substrates (glass, silicon, plastic,etc.). Numerous layers of the device can be fabricated and then thelayers assembled to form the final analysis tool. Channels can be etchedin single or multiple dimensions enabling more complicated chemicalseparation and detection. Such devices can be used to introduce reagentsdirectly onto the chip or interfaced with automation equipment for suchpurposes. Like all fluorogenic detection, these systems require anexcitation source.

SUMMARY OF THE INVENTION

Light based detection systems utilizing the processes described abovehave long been workhorses of chromatography systems and reaction vesselsincluding microarray scanners, microtiter plate readers, DNA sequencers,PCR and Q-PCR instruments, fluorescent microscopes, flow cytometeryinstruments and lab on a chip devices used in drug discovery and otherlife-sciences research. Light sources are integral components of thesebioanalytical tools. However, the lamps and lasers that power thesebioanalytical systems have presented engineering and cost constraintsthat limit sensitivity, reproducibility and robustness.

The present invention consists of one or more light sources in the formof a luminescent light pipe referred to herein as a lamp, in conjunctionwith relay optics for luminescence collection from an analyte forming aluminescence system for a volume interrogation apparatus wherein theinteraction of light with a chemical species located within or supportedon a solution volume can be the measure of the presence or quantitationof an analyte. Luminescence is defined as light not generated by hightemperature alone, typical of incandescence, including but not limitedto fluorescence and phosphorescence. Where high temperatures are definedas above approximately 2000° K. The analyte can be part of a reactioninvolving species including biopolymers such as, oligonucleotides (DNA,RNA iRNA, siRNA), proteins (including antibodies, enzymes, agonists,antigens, hormones, toxins), oligosaccharides and non polymeric speciessuch as steroids, lipids, phospholipids, small organic signalingmolecules (e.g., retinoic acid), pesticides and non peptidic toxins,hormones and antigens.

In alternative embodiments of the present invention, a lamp, inconjunction with relay optics for luminescence collection, form aflexible and efficient luminescence system for a capillary/fluorescenceapparatus. In an embodiment of the invention, a plurality of lightsources and fiber optic systems separately and simultaneously irradiatea plurality of capillaries with selected wavelengths of light and thefluorescence produced by the molecules flowing within the capillariescan be separately and simultaneously detected.

While lamps and lasers are key components in the biochemical reactorinstrument design each is best suited to unique applications withcompromises based on inherent performance traits. Typically lampsproduce broad-spectrum spontaneous emission but due to their largeangular output collection efficiency is poor. Large power densities aredifficult to attain; moreover accessing discrete wavelengths usingfilters and lenses results in dramatic power losses. Lasers can producelarge power outputs at discrete wavelengths based on stimulatedemission; however, intensity and spatial modulation is difficult andcostly. As well, the number of available discrete wavelengths islimited. The design and cost effective production of bench top andpoint-of-care analyzers is limited by this current pool of lightgenerators.

Traditional lamps and lasers are the most frequently employed lightgenerators in bioanalytical microfluidic instrumentation. While lampsand lasers are key components in the instrument design each is bestsuited to unique applications with compromises based on inherentperformance traits. Typically lamps produce broad-spectrum spontaneousemission but due to their large angular output, collection efficiency ispoor. Further, large power densities are difficult to attain. Moreover,accessing discrete wavelengths using filters and lenses results indramatic power losses. Lasers can produce large power outputs atdiscrete wavelengths based on stimulated emission, however, intensityand spatial modulation is difficult and costly. In addition, the numberof available discrete wavelengths is limited. The design and costeffective production of bench top and point-of-care analyzers is limitedby the current light generators.

Lamp

In various embodiments of the present invention, a lamp emitswavelengths of light, which excite fluorescence from photosensitivetargets in the sample of interest. In various embodiments of the presentinvention, a lamp can be in the form of a tube, rod, or fiber of varyingor constant diameter and varying or constant curvature. The crosssection can be circular, square or rectangular and can be constant orvarying. In various embodiments of the present invention, a constituentlight pipe can be made of glass, plastic, single or multiple inorganiccrystal(s), or a confined liquid. In various embodiments of the presentinvention, a pipe either contains or can be coated with a layer orlayers containing, a narrow band luminescent material such as organic orinorganic compounds involving rare earths, transition metals ordonor-acceptor pairs. In various embodiments of the present invention, alamp emits confined luminescence when excited by IR, UV, or visiblelight from an LED, laser, fluorescent tube, arc lamp, incandescent lampor other light source. In an embodiment of the present invention, a lampoperates through the process of spontaneous emission, which results in amuch larger selection of available wavelengths than can be available forefficient stimulated emission (laser action). In an alternativeembodiment, electrons or other radiation are used to excite theactivator and thereby the light pipe.

In an embodiment of the invention, light pipes will incorporate organicluminescent material referred to as plastic scintillators, doped oractivated plastic optical fibers or wavelength shifting plastics asdescribed by Albrecht, M. et al., in “Scintillators and WavelengthShifters for the Detection of Ionizing Radiation”, Nuclear ScienceSymposium Conference Record, 2003 IEEE, Volume 2, Issue: 19-25 Oct(2003) 1086 and Pla-Dalmau, A. et al., “Low-cost extruded PlasticScintillator”, Nuclear Instruments and Methods in Physics Research A,466 (2001) 482 both of which are hereby expressly incorporated byreference in their entireties. These materials are commerciallyavailable through Kuraray, Saint-Gobain and Eljen Technology. The hostmaterial can be typically made from polymethylmethacrylate or acrylic(PMMA), polyvinyltoluene, or polystyrene. There are numerous fluorescingdopants available enabling these materials to emit across the visiblefrom 400 to 650 nm. The best dopant for the Argon Ion laser replacementis K27. The plastic material can take on any geometric shape includinguncladded fiber, cladded fiber, tubes and rods with circular, square orrectangular cross section which can be constant or varying. The tubesand rods can have constant or varying curvature and have a constant orvarying diameter.

Relay Optics

In an embodiment of the present invention, relay optics consist of lightpipes, optical fibers, lenses and filters, which optically transport thelight from a lamp to one or more capillaries and light pipes, opticalfibers, lenses and filters which collect and transport any generatedfluorescence to an appropriate detector or array of detectors, inconjunction with adaptors for coupling the excitation light into thecapillaries, coupling the emission light out of the capillaries and forenhancing physical discrimination of the excitation and emission. In anembodiment of the present invention, relay optics, including fibers, canbe constructed in a loop or as a cavity so that light from a lamp canpass through one or more capillaries multiple times to enhanceexcitation efficiency.

In an embodiment of the present invention, a number of lamps eachemitting one or more color of light can have their constituent lightpipes coupled in parallel or in series acting to produce multiple colorssimultaneously or in sequence. In an embodiment of the presentinvention, one or more lamps can illuminate single channels, multipleparallel channels, multiple channels in multiple dimensions, numerousspots along the analysis channel and/or reservoirs connected to the flowstreams.

In an embodiment of the present invention, lamps can be irradiatedcontinuously during the measurement process or can be pulsed on and offrapidly to enable time-based detection methods. In an embodiment of thepresent invention, a lamp can be switched off between measurements, toeliminate the heat output. This can be contrasted with alternatives suchas arc lamps or lasers that are unstable unless they are operatedcontinuously.

Luminescence and Collection System

In an embodiment of the present invention, a flexible luminescence andcollection system for capillary/fluorescence apparatus allows for avarying number of samples to be analyzed simultaneously.‘Simultaneously’ is herein defined as occurring close in time. Two lightpipes can irradiate two capillaries at the same time and thefluorescence from the molecules in one of the capillaries can be delayeddue to physical or chemical effects relating to absorption,phosphorescence and/or fluorescence resulting in a delay in thefluorescence from the molecules in one of the capillaries. Thisexcitation can be still considered to result in ‘simultaneousdetection’. In an embodiment of the present invention, a luminescenceand collection system can be adjusted for uniform luminescence ofmultiple capillaries or wells or a large area including numerous wells,spots or channels as ‘detection volumes’. In an embodiment of thepresent invention, luminescence systems can irradiate an array ofchannels in an array of capillaries. In an embodiment of the presentinvention, an array of channels can be etched, molded, embossed into thecapillaries. In an embodiment of the present invention, a set of wellsintimately connected to fluidic conduits can be stepped along the lengthof the fluidic conduit such that they can be interrogated at numeroussites for the purposes of creating a map or image of the reactingspecies.

In an embodiment of the present invention, a luminescence and collectionsystem can irradiate an array of wells, spots and or an array ofchannels (be they etched, molded or embossed) or a set of wellsintimately connected to fluidic conduits such that they can beinterrogated at numerous sites for the purposes of creating a map orimage of the reacting species.

In an embodiment of the present invention, a luminescence and collectionsystem can irradiate homogeneous reactions within fluidic conduits orreservoirs; to irradiate heterogeneous reactions on the surface offluidic conduits or reservoirs; to irradiate homogeneous orheterogeneous reactions on the surface of or within the pores of aporous reaction support.

In an embodiment of the present invention, a luminescence and collectionsystem can emit multiple colors as desired. In an embodiment of thepresent invention, a luminescence and collection system can be pulsed onand off as desired to reduce heat generation. In an embodiment of thepresent invention, a luminescence and collection system can be pulsed onand off to allow time-based fluorescence detection.

In an embodiment of the present invention, a luminescence and collectionsystem can detect one or a number of reactions within the detectedvolume or volumes. The narrow band source of the light pipe drivenanalyzer provides better specificity, higher sensitivity, and lowerbackgrounds signals. The light pipe driven analyzer easily accommodatesmultiple wavelengths by additions of serially connected components.

In an embodiment of the present invention, a luminescence and collectionsystem can be pulsed on an off as desired to reduce or control heatgeneration and to allow time-based fluorescence detection.

In an embodiment of the present invention, luminescence systems canirradiate homogeneous reactions within fluidic conduits or reservoirs.In an embodiment of the present invention, luminescence systems canirradiate heterogeneous reactions on the surface of fluidic conduits orreservoirs. In an embodiment of the present invention, luminescencesystems can irradiate homogeneous or heterogeneous reactions on thesurface of or within the pores of a porous reaction support.

Other objects and advantages of the present invention will becomeapparent to those skilled in the art from the following description ofthe various embodiments, when read in light of the accompanyingdrawings.

BRIEF DESCRIPTION OF THE FIGURES

Various embodiments of the present invention can be described in detailbased on the following figures, wherein:

FIG. 1 shows a schematic drawing of system with multiple luminescentlight pipes connected to optical fibers which interface with capillariesthrough fiber capillary adapters and fluorescence collection optics;

FIG. 2A shows a schematic drawing (of a luminescent pipe viewed end on)of an LED pumped lamp. The lamp can be based on a fiber coiled around alinear array of LEDs;

FIG. 2B shows a schematic drawing (of a luminescent pipe viewed side on)of a bar of LED's exciting a luminescent light pipe in the form of anoptical fiber;

FIG. 3 shows a schematic drawing (of a capillary viewed end on)illustrating the interface between the fiber optics and the capillaries;

FIG. 4 shows a schematic drawing (of a capillary viewed end on)illustrating the interface between the fiber optics and the micro lensoptical element and the capillaries;

FIG. 5 shows a schematic drawing (of a capillary viewed end on)illustrating the interface between a one-dimensional array ofcapillaries from two optical fibers mated perpendicular to the entirearray. The light can be coupled from each fiber to the capillary arrayvia a light pipe adapter. In this manner, the same excitation lighttravels perpendicular through all the capillaries;

FIG. 6A shows a schematic drawing (side view) illustrating an ellipticalreflector with a luminescent light pipe positioned at one focus of anelliptical reflector and a UV lamp located at the other focus;

FIG. 6B shows a schematic drawing (top view) illustrating an ellipticalreflector with a luminescent light pipe positioned at one focus of anelliptical reflector and a UV lamp located at the other focus;

FIG. 7A shows a schematic drawing (side view) illustrating an ellipticalreflector with a luminescent light pipe positioned at one focus of theellipse and a linear array of LED's positioned at the other focus of theellipse;

FIG. 7B shows a schematic drawing (top view) illustrating an ellipticalreflector with a luminescent light positioned at one focus of theellipse and a linear array of LED's positioned at the other focus of theellipse;

FIG. 8 shows a schematic drawing (top view) illustrating an ellipticalreflector with a multi color luminescent light pipe positioned at onefocus and a linear array of LED's positioned at the other focus of theellipse;

FIG. 9 shows a schematic drawing of system with multiple luminescentlight pipes connected to optical fibers which provide emission to eachwell and separate fibers that collect emission from each well;

FIG. 10 shows a schematic drawing of a system with multiple luminescentlight pipes. The excitation can be delivered to each well via amicro-lens array. The emission can be collected by the same lens array.The excitation and emission are separated using a dichroic beamsplitter;

FIG. 11 shows a schematic drawing of a compound integrated opticalarray. The excitation and emission are delivered to each well via aconical protrusion into each well. This protrusion consists of a centralpipe surrounded by a conical external section. The central pipe can havean index that can be lower than the surrounding area and can be hollow.Excitation can be delivered to each well via the conical section whileemission can be collected by the central pipe;

FIG. 12 shows a schematic drawing an integrated optical array consistingof a transparent coupling plate with “dimples”, hemispheres or othersurface modifications which cause light to leave the light pipe andenter each well. The dimples are designed to represent a small fractionof the transparent window above each well;

FIG. 13A and B shows side view and top view respectively of schematicdrawings of a transparent micro-titer plate excited by one or moreluminescent light pipes. The plate serves as both a micro-titer plateand a coupling plate. The plate can consist of a series of internallight pipes connecting subsets of wells (the schematic illustrates fourparallel sections);

FIG. 14 shows the luminescence emission of a Terbium doped glassprototype when excited by UV light;

FIG. 15 shows a schematic drawing of a light pipe encased by acylindrical chamber which feeds off a linear LED array.

DETAILED DESCRIPTION OF THE INVENTION

The detection volume in the form of a well of fluid, a spot of fluid, achannel containing fluid or a reservoir attached to a channel containingfluid will all be referred to herein as the “detection volume”. The term“detection volume” can also refer to any of the afore mentionedconstructs in which the reaction for detection occurs in freelydiffusing solution, in a gel or polymer, attached to a surface,contained within a pore, or in some subsection of the entire wellvolume. As seen in FIG. 9, one example of the present inventioncomprises a plurality of lamps (908) with filters (910) for selectingthe wavelength of choice, in conjunction with a device for coupling(920) the lamps into multiple optical fibers, multiple optical fibersfor transferring the excitation light to the wells, adapters forcoupling light from the fibers into the detection volumes (914) locatedin a microtiter plate (924) and for coupling fluorescence from thedetection volumes into collection fibers, and collection fibers fortransferring the emitted light to a detector array. The term “emittedlight” is defined as including fluorescence, phosphorescence,reflection, diffraction and deflection resulting from the luminescence.

In an embodiment of the present invention, the source can be coupled tothe detection volumes using a special adapter. The adaptersimultaneously provides for coupling of fluorescent emissions from thesamples to the detection system.

In an embodiment of the present invention, the excitation light andemission light can be separately coupled from the bottom, side, or topof any or all detection volumes as preferred.

In an embodiment of the present invention, the optical fibers used fortransferring the excitation or emission can be made of glass, plastic, aconfined liquid or any other type of light pipe. The coupling adaptercan be made of glass, plastic, a confined liquid or any other suitablematerial.

In another embodiment of the present invention, two excitation transferfibers and the lamp can be connected in a loop so that light can passrepeatedly around the loop until absorbed by the detection volume. Inanother embodiment the coupling adapter can contain reflective regionswhich reflect unused excitation light back into the relay fiber or whichform a cavity so that unused light passes repeatedly through thedetection volume.

In other embodiments of the present invention, the excitation oremission light can be coupled to fibers using small lenses with orwithout a larger relay or projection lens.

In other embodiments of the present invention, the specific geometry ofthe source, fibers, wells and detection elements can be changed to anypracticable arrangement. Lenses used can consists of multiple elements,of both positive and negative power, and can contain glass and/orplastic elements. In alternative embodiments Fresnel lenses or adiffractive optics can be used.

In various embodiments of the present invention, the light from separatelamps can impinge on separate detection volumes or the light from onelamp can excite multiple detection volumes at once.

In an embodiment of the present invention, the number of samplesilluminated can be varied by varying the number of lamps, which areactive. The lamp can be activated during measurements and turned off atother times to minimize the heat generated.

In an embodiment of the present invention, each lamp contains aluminescent praseodymium doped YAG single crystal fiber or other dopedsingle crystals or rod of the same diameter as the delivery fiber. Inanother embodiment each lamp contains a luminescent praseodymium dopedglass fiber or rod of the same diameter as the delivery fiber. Inanother embodiment, each lamp contains a luminescent doped plasticoptical fiber or rod of the same diameter as the delivery fiber. Thefibers and rods can have a circular, square or rectangular crosssection. Also, the fiber or pipe diameter can be smaller or larger thanthe delivery fiber and then optically coupled to the delivery fiberusing for example a tapered cone.

In another embodiment of the present invention, some lamps can containalternate materials to allow for the generation of other colors,including infrared and ultraviolet. In one embodiment, these lamps ofalternate colors are connected in parallel so that different colors areimaged to different detection volumes. In another embodiment thealternate color lamps are connected in series so that the light of eachcolor passes through the constituent light pipes of lamps of differentcolors so that each detection volume can be illuminated by light of oneor more alternate colors at any given time. In another embodiment thelamp can contain one or more materials capable of producing luminescenceat more that one wavelength. As an example, multiple rare earth metalatoms can be doped into a glass host and multiple organic emitters canbe doped into a plastic host. In this embodiment, different pump sourcessuch as different color LEDs can be turned on or off to cause theproduction of the different colors.

In other embodiments of the present invention, relay fibers can be usedto direct different wavelengths of light on a detection volume atdifferent positions thereby allowing simultaneous detection of differentspecies present in the detection volume. These different excitationfibers can be positioned to allow detection of species at earlier orlater times during the procession of the reaction. In this or otherembodiments emission can be collected from more than one region of thedetection volume.

In other embodiments of the present invention, the lamp can contain aluminescent fiber of larger or smaller diameter than the delivery fiberwith provision for efficient coupling of the two.

In another embodiment of the present invention, the lamp can contain alarger diameter hollow fluorescent tube, which can be “necked down” indiameter to match the delivery fiber.

In another embodiment of the present invention, the lamp can contain alarge fluorescent rod, which can be coupled to more than one deliveryfiber.

In various embodiments of the present invention, the fibers, rods ortubes form light pipes that can be coated with one or more layers ofluminescent material in thick or thin film form. Praseodymium or otherrare earth doped lanthanum oxysulfides can be utilized as the film.

In another embodiment of the present invention, the lamp can contain atube, which contains within it a luminescent material in powder, liquidor other form.

In various embodiments of the present invention, the luminescent lightpipe can be of an appropriate cross sectional shape and can be freestanding or constructed on a substrate.

Potential luminescent materials suitable for use in this inventioninclude, but are not limited to, CRT or lamp phosphors including all ofthe lanthanides doped into lanthanum, yttrium, or gadolinium oxides oroxysulfides, or other phosphors with suitable emissions. One can easilygenerate a wide range of colors based on readily available and knownphosphor chemistries. This wide range of colors matches the numerouswidely accepted and commonly used fluorophors for bioanalyticalapplications. Other suitable materials include all of the lanthanidesdoped into a glass, an organic material containing one of thelanthanides, or a confined solution containing lanthanides.

In alternative embodiments of the present invention, the lamp can beswitched on and off rapidly so that a time varying excitation can beproduced. The color of the excitation can also be rapidly varied. Theserapid variations in excitation can be used in conjunction withtime-based detection to increase system sensitivity or to allow for thediscrimination of differing numbers, types, or states of fluorescencetargets.

In an embodiment of the present invention, the luminescent fiber orfibers of praseodymium doped glass or doped plastic optical fiber areexcited (pumped) by an array of LEDs with strong emission near 450 nm inwavelength as shown in FIG. 2. In alternative embodiments of the presentinvention, the pump source can be replaced with one or more similardevices such as other color LEDs, fluorescent lamps, semiconductor orsolid-state lasers, arc lamps, or incandescent lamps.

Another lamp embodiment uses an outer waveguide to deliver pump energyto the luminescent pipe. The pipe can be located at the center of theouter or pump waveguide and LEDs are located at either end. The pumpwaveguide may be filled with a solid, liquid, or gas whose refractiveindex can be lower than the index of the luminescent pipe. The outersurface of the pump waveguide may be metalized to minimize losses. Theluminescent pipe can be positioned in any orientation of the pipe. Thisorientation can be chosen to maximize the absorption of the excitationlight inside the pipe. The luminescent material can be formed into anyshape including fibers. More than one pipe emitting more than one pumpwavelength can use the same pump waveguide. Different luminescent pipescan be excited by activating different excitation LEDs.

Another embodiment, which emits multiple colors when excited by a lineararray of LEDs, is shown in FIG. 7. The pump energy can be delivered tothe luminescent pipe using an elliptical cavity geometry. Theluminescent pipe can be located at one focus and the excitation can belocated at the other focus. This geometry also works for a single colorpipe.

In another embodiment of the present invention, the excitation can bedelivered to each detection volume via a micro-lens array as shown inFIG. 10. A plurality of lamps (1008) with filters (1010) for selectingthe wavelength of choice, in conjunction with a device for coupling(1020) the lamps and magnifying the luminescence with a lens system(1015) and a dichroic beam splitter (1018) for transferring theexcitation and emission light to the micro lens array adapter (1022),for coupling luminescence into the wells (1014) in the microtiter plate(1024). The emission can be collected by the same lens array. Theexcitation and emission can be separated using the dichroic beamsplitter (1018).

In another embodiment of the present invention, the excitation light canenter a single coupling plate which can be designed to distribute lightto the individual detection volumes for analysis while simultaneouslycollecting emitted light for detection as shown in FIG. 11. In thisembodiment, excitation can be delivered from the luminescent light pipe(1130) to each detection volume and can be collected from each detectionvolume using a conical protrusion into each detection volume. Thisprotrusion consists of a central pipe (1134) surrounded by a conicalexternal section. The central pipe can have an index that can be lowerthan the surrounding area and can be hollow and coated with a reflectivelayer. Excitation can be delivered to each detection volume via theconical section while emission can be collected in the central pipe. Amirror (1138) can be used to increase the luminescence in the lightpipe. This device couples light into a microtiter plate and collects theemission (not shown). The analyte in each detection volume delivers theexcitation light to each well (not shown). The emission from each wellcan be collected in a central light pipe (1136) and transmitted normalto the surface above the central light pipe (1136). The excitation light(1140) is delivered through a conical protrusion (1132) into eachdetection volume. The luminescence from each detection volume iscollected by a central light pipe (1136) and directed towards thedetector. A scattering or reflective surface (1134) is used tohomogenizes the light distribution across the microtiter plate.

In other embodiments of the present invention, more than one couplingplate can be used with each plate coupled to a subset of the completearray of detection volumes. These multiple coupling plates can beconnected to one excitation source or can be connected to distinctsources. The coupling plate(s) can be made of glass, plastic, a confinedliquid or any other suitable material. In an embodiment of the presentinvention, the plate(s) can provide uniform luminescence to eachdetection volume, uniformly collect the emission and minimize theemission crosstalk. Excitation uniformity can be increased by applying asurface treatment to the upper surface of the coupling plate. Improvedimaging of the emission can be obtained by providing a lens element onthe top side of the central section.

In another embodiment of the present invention shown in FIG. 12, atransparent coupling plate can be utilized which consists of a lightpipe (1236) with mirror (1238) and “dimples”, hemispheres or othersurface modifications (1232) which cause the light to leave the lightpipe and enter each detection volume. The dimples are designed torepresent a small fraction of the transparent window above eachdetection volume. In this manner, the emission (1240) is most likelygoing to be transmitted through the plate without scattering andtransferred to the detector (1250). The dimples can be designed so thatthey provide uniform luminescence to the detection volumes and minimizeemission crosstalk between the detection volumes. The dimples can be inthe shape of a retro-reflector so that light that is not transmitted canbe reflected back into the waveguide. In this embodiment emitted lightcan be collected by a lens or system of lenses which image through thecoupling plate. In other embodiments more than one coupling plate can beused with each plate coupling to a subset of the complete array ofdetection volumes. These multiple coupling plates can be connected toone excitation source or can be connected to distinct sources. Thecoupling plate(s) can be made of glass, plastic, a confined liquid orany other suitable material. The emission (1240) is shown leaving thepipe to enter the sample volume. The microtiter plate and thefluorescence are not shown.

In another embodiment of the present invention shown in FIG. 13A and B,a completely or partially transparent coupling plate (1324) can functionto define the detection volumes (1314) containing the analyte. Thecoupling plate can consist of a series of internal light pipes (1322)connecting subsets of detection volumes. The various internal lightpipes can be separated by opaque walls. This internal structure can bedesigned to provide uniform intensity to each detection volume andminimize emission crosstalk between the detection volumes. In thisembodiment emitted light can be collected by a lens or system of lenseswhich image the coupling plate or fibers can be used to collect lightfrom each detection volume. In other embodiments, more than one couplingplate can be used with each plate coupling to a subset of the completearray of detection volumes. These multiple coupling plates can beconnected to one excitation source or can be connected to distinctsources. The coupling plate(s) can be made of glass, plastic, a confinedliquid or any other suitable material.

In another embodiment of the invention shown in FIG. 15, a linear arrayof LEDs (1505) can be mounted on the external side of a cylinder. Thelight can be injected into the cylindrical chamber (1530) which containsthe luminescence light pipe (1508). The inside cylinder walls are highlyreflective and, as an example, could be coated with Oerlikon Silflex.This design maximizes the amount of reflective surface surrounding thelight pipe. The pipe can be located at any location an orientationwithin the cylinder to maximize the amount of LED light that can beabsorbed.

In other embodiments of the present invention, some of the light sourcescan emit infrared light and be used to heat detection volumes as part ofthe analysis process.

As shown in FIG. 1, in an embodiment of the present invention, aplurality of lamps (108) with filters (110) for selecting the wavelengthof choice, in conjunction with a device for coupling (120) the lampsinto multiple optical fibers (112), multiple optical fibers fortransferring the excitation light to the capillaries (132) (note 132points to the bore of the capillary), adapters for coupling light fromthe fibers into the capillaries (122) and for coupling fluorescence fromthe capillaries into collection fibers (124) and collection fibers (116)for transferring the emitted light (118) to a detector array (notshown). In an embodiment of the present invention, fibers for couplingfluorescence from the capillaries can be placed at 90° to the excitationfibers (as shown in FIG. 3).

In an embodiment of the present invention, a luminescent light pipe canconsist of a pipe coupled to a transparent fiber. In an embodiment ofthe present invention, a luminescent pipe can be a continuous fiber,which can directly deliver the luminescence to one or more capillariesor be coupled to a transparent fiber. In an embodiment of the presentinvention, a luminescent pipe can consist of a luminescent rod.

In an embodiment of the present invention, a coupling optic can containa filter to narrow excitation spectrum.

In an embodiment of the present invention, the coupling adapter cancontain reflective surfaces, which reflect light passing through thecapillary back into the capillary. These reflecting surfaces may form aring cavity or other form of cavity with the result that excitationlight passes repeatedly through the flow region of the capillary. In anembodiment of the present invention, the reflective surfaces aredesigned to enhance both the excitation and emission intensity. In anembodiment of the present invention, the width of a reflective ring canbe 1.5 times the diameter of the capillary. In an embodiment of thepresent invention, the width of a reflective ring can be 1.5 times thespot size. In an embodiment of the present invention, the reflectivering can be 60 microns-100 microns in width. In an embodiment of theinvention the spot size can be 40-60 microns.

In an embodiment of the present invention, one or more LED's (207) inparallel are used as a lamp source (see FIG. 2A which shows aluminescent pipe (201) viewed end on and FIG. 2B which shows aluminescent pipe viewed side on) mounted inside a housing (262)directing the light towards the sample (214). In this example, theluminescent light pipe can be a continuous fiber wrapped around a lineararray of LEDs. In various embodiments of the present invention thelength of the luminescent pipe can be extended and the number of LED'sin parallel increased in order to increase the intensity of theluminescent pipe. LED's have a number of advantages for incorporationinto a luminescent pipe including their engineering simplicity, longlife, low manufacturing cost, flexible emission wavelengths and highlight output power. In an embodiment of the present invention, more thanone luminescent pipe can be excited by the same LED source. In anembodiment of the present invention, a luminescent pipe can generatemore than one color.

In an embodiment of the present invention, a source can be coupled tothe capillaries using a special adapter assembly for coupling this lightinto the capillary system. In an embodiment of the present invention, anadapter assembly can also simultaneously provide for coupling offluorescent emissions from the samples to the detection system.

In various embodiments of the present invention, optical fibers used fortransferring the excitation or emission can be made of glass, plastic, aconfined liquid or any other type of light pipe. In various embodimentsof the present invention, a coupling adapter can be made of glass,plastic or any other suitable material.

In various embodiments of the present invention, a capillary can be usedas a light pipe for transferring either the excitation or emission lightto or from the active region.

In an embodiment of the present invention, two excitation transferfibers and the lamp can be connected in a loop so that light can passrepeatedly around the loop until absorbed by the capillary. In anembodiment of the present invention, a coupling adapter can be designedto collimate the excitation light so that it can pass from the fiber onone side of the capillary to be easily collected by the fiber on theopposite side of the capillary. In an embodiment of the presentinvention, the coupling adapter can contain reflective regions, whichreflect unused excitation light back into the relay fiber. In anembodiment of the present invention, the coupling adapter can containreflective regions, which form a cavity so that unused light passesrepeatedly through the flow region of the capillary.

In another embodiment of the present invention, as seen in FIG. 5, alight pipe adapter can function as an extension of the excitationtransfer fiber or light pipe causing light to impinge on more than onecapillary (532) (note 532 points to the bore of the capillary) from theside. In this embodiment, one of the ends of light pipe adaptor canserve as a retro reflector to increase the intensity in the capillaries.

In another such embodiment of the present invention, light enters fromboth ends (540 and 542) of the adapter. In this embodiment of thepresent invention one or more optical fibers deliver excitation from oneor more luminescent pipes to the capillary light pipe adapter from twodirections. Light propagates through the adapter and out the oppositefiber. Light can travel back around through one or more luminescentpipes and re-enter the capillaries. The light pipe adapter can bedesigned to efficiently pipe the light from one end of the pipe to theother.

In various embodiments of the present invention, the light pipe adapterfunctions to relay the light to any number of capillaries and throughmultiple reflections to make the luminescence uniform. Therefore, thelight (540) piped by the adapter (546) can be transferred to multiplecapillaries with great uniformity.

In an embodiment of the present invention, an adapter (546) can besufficiently wide so that the capillaries fill region that is smallerthan the adapter. In another embodiment of the present invention, alight pipe adapter can be narrower than the capillaries. In this case,the light pipe adapter acts as a bridge to carry light from onecapillary to the next capillary.

In various embodiments of the present invention, a light pipe adaptercan have its surface treated (550) to internally reflect light directlyinto the multiple flow regions. This treatment can consist of mechanicalgrooves, holographic patterning and thin film multi-layer dielectrics.This treatment can be made to be wavelength selective allowing thefluorescence emission from the capillaries to preferentially leave thelight pipe adaptor at a specific angle. Such treatments are particularlyuseful when achieving uniformity over a relatively few number ofcapillaries.

In an embodiment of the present invention, emission can be collected byfibers mated to each capillary. The collection fiber (544) leads to thedetector (not shown) in FIG. 5.

In an embodiment of the present invention, the coupling adapter can bemade of material which can be index matched to the capillary body,causing the capillary body to function as part of the adapter. Inanother embodiment of the invention, material of the adapter can beindex matched to the flowing liquid inside the capillary. In anotherembodiment of the present invention, an adapter can replace thecapillaries with the flow proceeding through the adapter. In anotherembodiment, the adapter can consist of a hollow structure filled with anindex matching fluid matched to the capillary body or flowing fluid. Theadapter can be made using standard etching technologies.

In another embodiment, the light pipe adapter can be used with otherlight sources including edge emitting LEDs and lasers.

In various embodiments of the present invention, the excitation (340) oremission (336) light can be coupled to fibers with or without a largerrelay or projection lens. One example is shown in FIG. 3. In anembodiment of the present invention, a collection fiber (334) may beused to collect the emission light (336) from one or more capillaries(332) (note 332 points to the bore of the capillary) directly to adetector or an array of detectors. With the exception of the couplingoptic (322), the capillary surface (330) can be surrounded by the ringreflector (338).

In various embodiments of the present invention, the excitation (440) oremission (436) light can be coupled to fibers using small lenses with orwithout a larger relay or projection lens. One example is shown in FIG.4. In an embodiment of the present invention, a lens (442) may be usedto image the emission light (436) from one or more capillaries (432)(note 432 points to the bore of the capillary) directly to a detector oran array of detectors. With the exception of the coupling optic (422),the capillary surface (430) can be surrounded by the ring reflector(438).

In various embodiments of the present invention, the specific geometryof the source, fibers, capillaries and detection elements can be changedto any practicable arrangement. In various embodiments of the presentinvention, lenses used can consist of multiple elements, of bothpositive and negative power, and can contain glass and/or plasticelements. In an embodiment of the present invention, Fresnel lenses canbe used. In an embodiment of the present invention, diffractive opticscan be used.

In an embodiment of the present invention, the light from separate lampscan impinge on separate capillaries. In an embodiment of the presentinvention, the light from one lamp can excite multiple capillaries. Inan embodiment of the present invention, the light from one lamp cansimultaneously excite multiple capillaries.

In an embodiment of the present invention, the number of samplesilluminated can be varied by varying the number of lamps, which areactive. In an embodiment of the present invention, a lamp will beactivated during measurements and turned off at other times to minimizethe heat generated.

In an embodiment of the present invention, rare earth activated glasscan be used as light pipes. In one embodiment of the invention Terbium(Tb) is used to dope the glass rods used as a light pipe. In anotherembodiment of the invention, Praseodymium (Pr) is used to dope the glassrods used as a light pipe. Table 1 gives a list of some commonrare-earth-dopants in the UV spectra and the examples of emissionwavelength ranges.

In an embodiment of the present invention, a lamp can contain alternatematerials to allow for the generation of other colors, includinginfrared and ultraviolet. FIG. 6 shows a luminescent pipe (652)positioned at one of the two foci of an elliptical cavity with one lightsource (654) positioned at the other focus. This light source can be aUV lamp used to excite the light pipe. A back mirror (656) and couplingoptic (652) are shown in FIG. 6. The coupling optic is shown as 658.FIG. 7 shows a luminescent pipe (752) positioned at one focus of anelliptical cavity with a linear array of LED's (754) positioned at theother focus. A back mirror (756) and coupling optic (752) are also shownin FIG. 7. The coupling optic is shown as 758. TABLE 1 List of commonrare-earth-dopants, their hosts and examples of emission wavelengthranges. Rare Earth Important emission Dopant Common host glasseswavelengths (nm) neodymium (Nd) silica, phosphate glass 1030-1100,900-950, 1320-1350 ytterbium (Yb) silica 1000-1100 erbium (Er) silica,phosphate glass, 1500-1600, 2700, 550 fluoride glasses thulium (Tm)silica, fluoride glasses 1700-2100, 1450-1530, 480, 800 praseodymium(Pr) silica, fluoride glasses 1300, 635, 600, 520, 490 terbium (Tb)silica 489, 547, 589, 622 europium (Eu) silica  610 holmium (Ho) silica2100

FIG. 8 shows a multi color luminescent pipe (855) positioned at onefocus of an elliptical cavity with a linear array of LED's (854)positioned at the other focus. A back mirror (856) and coupling optic(858) are also shown in FIG. 8. In an embodiment of the presentinvention, lamps of alternate colors are connected in parallel so thatdifferent colors are delivered to different capillaries. In anembodiment of the present invention, alternate color lamps are connectedin series so that the light of each color passes through the constituentlight pipes of lamps of different colors so that each capillary can beilluminated by light of one or more alternate colors at any given time.In an embodiment of the present invention, lamp can contain one or morematerials capable of producing luminescence at more that one wavelength.In an embodiment of the present invention, different pump sources suchas different color LEDs can be turned on or off to cause the productionof the different colors.

A was constructed in which a Tb doped glass rod was the luminescentpipe. The Tb glass rod was surrounded with five GE® Germicidal lamps(model G8T5, which each emit 2.1 W of UV light) positioned equidistantaround the luminescent pipe. These UV lamps emitted radiation at awavelength of 254 nm. At this wavelength, these lamps were germicidal(an agent that is destructive to pathogenic micro-organisms). The outputof the light source subsystem containing the Tb doped glass light pipeis shown in FIG. 14 where an intense fluorescence emission is observedaround 550 nm with a total power of 400 mW (the linewidth at 550 nm was12 nm and the power was 240 mW). In the prototype, the Tb doped glassfluorescence produces an intense green beam of light which can beconnected using a fiber optic tube to the capillary electrophoresisexperiment. After one UV lamp is turned on, the fluorescence emission isobserved. The fluorescence emission can be incrementally increased asthe remaining four UV lamps are successively turned on producing 10.5 Wof UV light. The fluorescence emission can be directed through thecapillaries and the wavelength can be absorbed by molecules derivatizedwith the Cy-3 fluorophore from Invitrogen™. Other wavelengths of lightcan be generated using rare earth doped glass to detect otherfluorophores conjugated with biological molecules of interest. Table 2includes a list of some common fluorophores and the absorption andemission maxima.

In an alternative embodiment of the invention, a Tb doped glass can bechosen as the luminescent pipe with five LED's positioned equidistantaround the luminescent pipe. In an alternative embodiment of theinvention, a Tb doped glass can be chosen as the luminescent pipepositioned at one focus of an elliptical cavity with a bar of LED'spositioned at the other focus. In an alternative embodiment of theinvention, a Pr doped glass can be chosen as the luminescent pipe withfive LED's positioned equidistant around the luminescent pipe. In analternative embodiment of the invention, a Pr doped glass can be chosenas the luminescent pipe positioned at one focus of an elliptical cavitywith a bar of LED's positioned at the other focus.

In an embodiment of the present invention, one or more optical fibersconnected to one or more capillaries through one or more coupling opticsconnect with the capillaries at one or more locations in space. In anembodiment of the present invention, a species flowing through acapillary can be first excited at one location and the absorption orsecond excitation resulting from the first excitation can be measured ata second location. In an embodiment of the present invention,differences in the absorbed or emitted light with respect to space canbe detected. In an embodiment of the present invention, differences inthe absorbed or emitted light with respect to time can be detected. Inan embodiment of the present invention, differences in the absorbed oremitted light with respect to frequency can be detected. TABLE 2 List ofsome exemplary fluorophores and their absorption and emission maxima.Absorption Emission Maximum (nm) Maximum (nm) Methoxycoumarin 340 405Coumarins 355 445 Fluorescein 494 518 Bodipy-F1 505 513 Ethidium Bromide518 605 Bodipy-R6G 528 550 Rhodamine 540 570 TAMRA 542 568 Cy-3 550 570Tetramethylrhodamine 555 580 Bodipy 565 571 ROX 574 602 X-rhodamine 580605 Texas Red 590 610 Naphthofluorescein 605 675 YOYO-3 612 631 Cy-5 649670

In an embodiment of the present invention, relay fibers can be used todirect different wavelengths of light on a capillary at differentpositions thereby allowing simultaneous detection of different speciespresent in the flow stream of a capillary. These different excitationfibers can be positioned to allow detection of species at earlier orlater times of elution from a capillary. In an embodiment of the presentinvention, emission can be collected from more than one region of acapillary.

In an embodiment of the present invention, a lamp can contain aluminescent fiber of larger or smaller diameter than a delivery fiberwith provision for efficient coupling of the two fibers.

In an embodiment of the present invention, a lamp can contain a largerdiameter hollow fluorescent tube, which can be “necked down” in diameterto match a delivery fiber.

In an embodiment of the present invention, a lamp can contain a largefluorescent rod, which can be coupled to more than one delivery fiber.

In an embodiment of the present invention, the fibers, rods or tubesform light pipes are coated with one or more thick layers of luminescentmaterial. In an embodiment of the present invention, the fibers, rods ortubes form light pipes are coated with one or more thin layers ofluminescent material. In an embodiment of the present invention, thefibers, rods or tubes form light pipes are coated with one or more thickor alternatively thin layers of luminescent material. Tb, Pr or otherrare earth doped lanthanum oxysulfide which can be utilized as a filmare examples.

In an embodiment of the present invention, a lamp can contain a tube,which contains within it a luminescent material in powder, liquid orother form.

In an embodiment of the present invention, a luminescent light pipe canbe of any appropriate cross sectional shape and can be free standing orconstructed on a substrate.

Luminescent material is defined as a material which can be activated toluminesce, including glass impregnated with rare earth dopants, glassimpregnated with transmetal dopants, organic polymers impregnated withrare earth dopants, organic polymers impregnated with transmetaldopants, inorganic polymers impregnated with rare earth dopants,inorganic polymers impregnated with transmetal dopants, organicemitters, inorganic emitters, CRT phosphors, lamp phosphors andscintillating material. In various embodiments of the present invention,luminescence materials can include one or more combinations of theluminescent material. In various embodiments of the present invention,luminescence materials can include all of the lanthanides doped intolanthanum, yttrium, or gadolinium oxides or oxysulfides, or otherphosphors and scintillators with suitable emissions. In variousembodiments of the invention, these rare earth dopants are used togenerate a wide range of colors based on available and known phosphorand scintillator chemistries. This wide range of colors matches thenumerous widely accepted and commonly used fluorophors for bioanalyticalapplications. In various embodiments of the invention, the light pipecan emit intense UV through to IR emission. Table 3 identifiescharacteristics of a light source subsystem which enhance theperformance for irradiating molecules present in a plurality ofcapillaries.

In various embodiments of the present invention, a lamp can be switchedon and off rapidly so that a time varying excitation can be produced. Inan embodiment of the present invention, the color of the excitation canalso be rapidly varied. In an embodiment of the present invention, theserapid variations in excitation can be used in conjunction withtime-based detection to increase system sensitivity. In an embodiment ofthe present invention, these rapid variations in excitation can be usedto allow for the discrimination of differing numbers, types, or statesof fluorescence targets.

In an embodiment of the present invention, the luminescent fibers of Prdoped YAG are excited (pumped) by an array of LEDs with strong emissionat 450 nm. In an embodiment of the present invention, the pump sourcecan be replaced with one or more similar devices such as other colorLEDs, fluorescent lamps, semiconductor or solid-state lasers, arc lamps,or incandescent lamps.

In an embodiment of the present invention, a lamp operates through theprocess of spontaneous emission, which results in a much largerselection of available wavelengths than can be available for efficientstimulated emission (laser action). TABLE 3 Performance EnhancingCharacteristics of Light Source Subsystem Feature Enabled ThroughAdvantage Bright/Powerful Stable source Allows for excitation ofnumerous material can be capillaries simultaneously, driven to producesufficient power to provide for high power in one excitation of few ormany or several detection volumes wavelengths Separate Individual lightIncreased specific fluorescence pipe to pump one excitation to eachcapillary; or numerous F1 Increased specific fluorescence excitationemission from each capillary; wavelengths Enhanced discrimination ofthrough each signals from several capillaries capillary SimultaneousEach light pipe Simultaneous analyses; Easy to pumping each implementmultiplexed analyses; capillary at the Increased speed of analyses; sametime Increased throughput Modulation On/Off of one or Rapid,reproducible and stable more LED's modulation of excitation; modulatesreproducible fluorescence signal fluorescence from capillaries afterOn/Off; emission strength results in facile discrimination betweenfluorescence signal and background and/or noise; allows for facilemultiplexed signal generation in time by modulation of source excitationSensitivity Increased Enhanced S/N; no need for fluorescence electronicsignal optimization emission strength to capillaries; combination withtime based detection Source Stability Attenuating or Feedback of lampoutput used to increasing the drive voltage of LED to give LED's output.constant power Spectra Stability Stability of Significantly morespectral spectral emission stability than that of 1) a laser from thewhich typically has color balance luminescent shifts over time and 2) anarc material for lamp which is notoriously example rare unstable earthdoped glasses, transmetal doped glasses and organic emitters DefinedChoice of one or Specific fluorescence emission is more rare earthnarrowly defined; Simultaneously dopants or serially; Excite differentemission output wavelengths that are not changing in time; Producesspecific fluorescence excitation wavelengths wavelength Variable Choiceof one or Produces specific fluorescence more rare earth excitationwavelengths; facilitates dopants multipexed analyses Durability Inherentstability Long term drift and or decay in of luminescent lamp outputeliminated source material Discrimination Controlled Distinguish number,type, or state modulation of of fluorescence labeled moleculesexcitation Low Heat Low heat Reduced heat in apparatus. generating LED'sand low thermal output of luminescent source material

In addition to chromatography systems and reaction vessels, the lightsource envisaged in this invention can be adapted for use in a varietyof life science research tools including microarray scanners, microtiterplate readers, DNA sequencers, PCR and Q-PCR instruments, fluorescentmicroscopes, flow cytometery instruments and total analysis systems inthe form of lab on a chip devices, optical sensors, medical devicesbased on luminescence, and miniaturized readers for therapeutic anddiagnostic applications.

The foregoing description of the various embodiments of the presentinvention has been provided for the purposes of illustration anddescription. It is not intended to be exhaustive or to limit theinvention to the precise forms disclosed. Many modifications andvariations will be apparent to the practitioner skilled in the art.Embodiments were chosen and described in order to best describe theprinciples of the invention and its practical application, therebyenabling others skilled in the art to understand the invention, thevarious embodiments and with various modifications that are suited tothe particular use contemplated. It is intended that the scope of theinvention be defined by the following claims and their equivalents.

Other features, aspects and objects of the invention can be obtainedfrom a review of the figures and the claims.

Separate and Simultaneous Irradiation: the light source subsystemprovides sufficient power to irradiate linear arrays and 2-D arrays ofanalysis wells or spots in parallel for high density applications.

Modulation: Simple electronics can be used to modulate the light sourcesubsystem at MHz rates. This capability allows for their use in analysesconducted in ambient light conditions. Analyses can be performed thatdiscriminate against background signals and produce enhanced signal tonoise ratios.

Moisture and Temperature Insensitivity: This is particularly importantfor remote sensing applications. The light source subsystem is stablefor a very broad range of environmental testing conditions.

Low Heat Production: Analytical complications associated with heatgenerated by non light source subsystem are eliminated. This isparticularly important for biological analyses.

Stability and Robustness: The color purity and intensity of the lightsource subsystem light output doesn't change as a function of howintensely they are driven nor does it change over time.

Modulation rates up to and even exceeding MHz can be achieved bymodulating the excitation source used to activate our glass. In anembodiment of the invention, LEDs are used to excite the luminescentmaterial. Therefore, modulating the LED will result in modulation of thelight source output. The circuitry for modulating an LED is well knownand typically consists of a square wave, sinusoidal wave or a pulsegenerator. The output of the generator is then fed to a transistoramplifier circuit which drives the LED.

It is to be understood that other embodiments of the invention can bedeveloped and fall within the spirit and scope of the invention andclaims

1. A method of analyzing one or more analyte comprising: (a) directingluminescence from of one or more wavelength from a light pipe includingone or more luminescent material onto the one or more analyte; and (b)directing light emitted from the one or more analyte onto one or morelight detector to analyze the one or more analyte.
 2. The method ofclaim 1, further comprising: (c) detecting the presence of the one ormore analyte; and (d) identifying a characteristic of the one or moreanalyte based on the light emitted from the one or more analyte.
 3. Anapparatus for analyzing one or more analyte comprising: (a) relay opticsfor directing luminescence of one or more wavelengths from one or morelight pipes including one or more luminescent material onto one or moreanalyte; (b) relay optics for directing emitted light from the one ormore analyte onto one or more light detector; and (c) one or moredetector for detecting the presence of the one or more analyte.
 4. Theapparatus of claim 3, wherein the one or more analyte undergoes anelectrochemical reaction prior to, during or after the luminescence. 5.The apparatus of claim 3, further comprising the step of identifying acharacteristic of the one or more analyte based on the detection of thelight emitted from the one or more analyte.
 6. The apparatus of claim 3,further comprising means for directing one or more flow of the one ormore analyte into one or more detection volume, wherein the luminescenceis directed onto the one or more detection volume and the light emittedby the one or more analyte is emitted from the one or more detectionvolume.
 7. The apparatus of claim 6, wherein the luminescence issimultaneously and separately directed to the one or more detectionvolume.
 8. The apparatus of claim 6, further comprising means forseparating the one or more analyte in the one or more flow whiledirecting the one or more flow into the one or more detection volume. 9.The apparatus of claim 8, wherein the separation of the one or moreanalyte is temporal with respect to the duration of time of the one ormore flow and the one or more analyte is detected at one or more elapsedtime.
 10. The apparatus of claim 9, further comprising identifying theone or more analyte based on detecting one or more of thecharacteristics selected from the group consisting of emitted lightwavelength, difference in emitted light wavelength, emitted lightintensity, difference in emitted light intensity, direction of emittedlight, difference in direction of emitted light, temperature,temperature change, potential, potential change, number of molecules,change in number of molecules, time elapsed and change in elapsed time.11. A system for identifying one or more analyte comprising: (a)directing the flow of the one or more analyte into one or more detectionvolume; (b) directing luminescence of one or more wavelengths from oneor more light pipe including one or more luminescence material throughrelay optics onto the one or more analyte; (c) directing emitted lightfrom the one or more analyte in the detection volume through relayoptics onto one or more light detector; (d) detecting the emitted lightof the one or more analyte using one or more light detector; and (e)identifying a characteristic of the one or more analyte based on thelight emitted from the one or more analyte.
 12. The identificationsystem of claim 11, wherein the one or more analyte present in thedetection volume undergoes a reaction selected from the group consistingof a heterogeneous reaction and a homogeneous reaction.
 13. Theidentification system of claim 11, wherein one or more of the analytepresent in the detection volume is contained in the detection volume.14. The luminescence system of claim 11, wherein one or more of theanalyte present in the detection volume is attached to one or moresurface of the detection volume.
 15. The luminescence system of claim11, wherein one or more of the analyte present in the detection volumeis photo-sensitive.
 16. The luminescence system of claim 11, wherein oneor more of the analyte present in the detection volume isthermo-sensitive.
 17. The luminescence system of claim 11, wherein thedetection allows the analyte to be quantitatively analyzed.
 18. Theluminescence system of claim 11, where in step (b) the relay opticsreflect luminescence that has passed over the one or more analyte backinto the relay optics.
 19. The luminescence system of claim 11, where instep (b) one or more light pipes are connected in series.
 20. Theluminescence system of claim 11, where in step (b) one or more lightpipes are connected in parallel.
 21. The identification system of claim11, wherein the detection volume can be selected from the groupconsisting of a well, micro-cuvete, a micro-titer plate, a micro-arraychip, a capillary, a tube, a pore, a sensor and a fluidic chip.
 22. Theidentification system of claim 11, wherein the emitted light can bedetected based on one or more properties of the light emitted selectedfrom the group consisting of fluorescence, phosphorescence, absorbance,transmittance, scattering and luminescence.
 23. The identificationsystem of claim 11, wherein the luminescence is generated at least inpart by a light pipe comprising: (a) a luminescent material, wherein oneor more components of the luminescent material is selected from thegroup consisting of: activated glass, plastic, single inorganic crystal,multiple inorganic crystals and a confined liquid; (b) an activator,wherein the activator is selected from the group consisting of organiccompounds doped with rare earths metal atoms, organic compounds dopedwith transition metal atoms, organic compounds doped with donor-acceptorpairs, organic compounds, inorganic compounds doped with rare earthsmetal atoms, inorganic compounds doped with transition metal atoms,inorganic compounds doped with donor-acceptor pairs, and inorganiccompounds; and (c) a source for exciting the activator.